U.S. President Barack Obama meets with Turkish President Recep Tayyip Erdogan (L) at the U.S. ambassador's residence during the World Climate Change Conference 2015 (COP21) in Paris, France in this December 1, 2015 file photo. Photo: Reuters/Kevin Lamarque

The U.S. government can do little for now but voice its concern as Turkish President Tayyip Erdogan uses a failed coup attempt to purge thousands of his opponents and demand the extradition of a dissident cleric living in Pennsylvania.

Erdogan's decision to allow the resumption of flights at the Incirlik Air Base, which is important in the United States' fight against Islamic State, has averted an immediate confrontation between the two allied countries.

But U.S. officials have been rattled by the extent of Turkey's response to the failed coup, and say the relationship going forward will depend on how Erdogan pursues the cleric, Fethullah Gulen, and how far the crackdown extends.

Still, Turkey's cooperation in the fight against Islamic State is of paramount importance to Washington in the uneasy alliance so, as in its dealings with repressive governments from Cairo to Beijing, the Obama administration finds itself trying to balance U.S. security interests against its human rights and democratic principles.

"What happens to our relationship with Turkey will largely depend on how Turkey itself works its way through the investigations and the decisions they make in the wake of this attempted coup," a senior U.S. official said.Erdogan has accused Gulen of being behind the coup and said on Monday that his government will formally request the cleric's extradition within days.

Gulen flatly denies any involvement in the coup. Some in the U.S. administration think the detention of thousands of military officers, police, judges and prosecutors in the wake of the failed plot already has been excessive.

"We believe Turkey has gone beyond what we wanted to see," a second official said, speaking on condition of anonymity.

U.S. Secretary of State John Kerry says Turkey has the right to prosecute those involved in the coup but, concerned about human rights and democracy in a key NATO ally, cautioned it against going too far.

"We stand squarely on the side of the elected leadership in Turkey. But we also firmly urge the government of Turkey to maintain calm and stability throughout the country," he said in Brussels on Monday.

European Union foreign policy chief Federica Mogherini called on Ankara to avoid steps that would damage the constitutional order.

At stake is Turkey's long-held hope to become part of the European Union, and Mogherini made clear that if Turkey imposed the death penalty it would be a deal breaker.

No leverage

As a practical matter, however, the United States and its allies may have no leverage over Turkey's internal affairs.

"There is nothing the U.S. government can do to dissuade President Erdogan from purging the Turkish military and judiciary from people he views as a threat," said Matthew Bryza, a former senior White House adviser on Turkey. "President Erdogan will simply do this, period. He views such measures as both a matter of survival and then as a means to significantly greater power."

In the short term at least, the United States and Turkey will be locked into a "transactional relationship," said Joshua Walker, a former U.S. diplomat and Turkey expert at the German Marshall Fund in Washington.

"I think that President Erdogan has made it very clear that they will do whatever it takes to - in their words - 'secure Turkey', and if that means leveraging Incirlik and other military bases, I'm convinced they will do it," said Walker.

"They say they won't discuss a Plan B because the U.S. is an ally but it's clear they have the leverage to shut down Incirlik, and this is their top security priority in the near term - Gulen and not ISIS," Walker added.U.S. defense officials said the electric power remains off at Incirlik but flight operations have resumed using generators. "They're working to restore power,” said one official.

Incirlik is host to a number of U.S. intelligence facilities that are critical to the fight against Islamic State.

Senior Turkish officials are set to attend an international meeting in Washington this week focused on the campaign against Islamic State.

Islamic State

While Turkey has joined the U.S.-led drive against Islamic State in Syria, Erdogan's government has been uncomfortable with U.S. backing of a Syrian Kurdish force, which it considers an appendage of the PKK, a Kurdish rebel group fighting for independence for Turkey's Kurds.

Differences over that issue, however, have eased as Erdogan has confronted a spate of attacks inside Turkey widely believed to have been carried out by Islamic State.As a result, there has been growing cooperation between Syrian rebel groups backed by Turkey and the United States fighting to end Islamic State control of a 60-mile long strip along the border with Turkey.

Soner Cagaptay, an analyst with the Washington Institute for Near East Policy, said the coup will significantly disrupt the campaign against Islamic State because it has divided the Turkish military, with many officers allegedly involved in the plot coming from the air force and the gendarmerie.

Significantly, the commander of the Incirlik air base, General Bekir Ercan Van, was among those detained over the coup.

Erdogan could threaten to close the Incirlik base to U.S. forces as part of his push for Gulen's extradition but Kerry has so far made clear that Turkey would need to provide convincing evidence of Gulen's involvement in any extradition request.

"Incirlik is important to the anti-ISIS struggle, but it's not indispensable," Cagaptay said. "If Washington feels that this becomes the sine qua non in the relationship, the U.S. might pull the plug out. It would require a repositioning of forces."